Antigen

Antigen Class

TFs and others

Antigen

ESR1

Cell type

Cell type Class

Breast

Cell type

Breast cancer cells

NA

NA

Sample

source_name

Breast cancer PDX HCI-005 tumour

tissue

PDX model HCI-005

time point

Short-term (5 days treatment)

chip antibody

ERα (HC-20)X (Santa Cruz SC-543X)

treatment

DHT

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Tumors were cut into 30µm slices on a cryostat and fixed with formaldehyde for 10m prior to quenching. Chromatin was prepared and subsequently sheared by the Diagenode BioRuptor Pico for 5.5 cycles (30 sec on, 30 sec off) on ice. Sheared chromatin was immunoprecipitated with ERα antibody overnight, after coupling to Protein A Dynabeads (10002D). DNA was purified using phenol:chloroform:isoamyl alcohol extraction. Libraries were prepared according to manufacturer's instructions accompanying the Qiagen Ultralow Input Library Kit (Part# 180495). ChIP-Seq; Illumina NextSeq500 (High Output v2) single-end 75 bp reads.

Sequencing Platform

instrument_model

NextSeq 500

hg38

Number of total reads

102415955

Reads aligned (%)

77.4

Duplicates removed (%)

7.3

Number of peaks

6831 (qval < 1E-05)

hg19

Number of total reads

102415955

Reads aligned (%)

76.7

Duplicates removed (%)

8.9

Number of peaks

6183 (qval < 1E-05)